Having trained at Cuddesdon near Oxford, Chapman was ordained as a deacon in the Church of England in 1889 and began a curacy in the parish of St Pancras, London. He found himself increasingly troubled during this time about the position of the Church of England and eventually left the parish soon after Trinity Sunday.[3]

In December 1890 Chapman was conditionally baptized in the Catholic Church at the Brompton Oratory. In April 1891 he entered the Jesuit novitiate at Manresa House, Roehampton (now Parkstead House), but after eight months had determined that his vocation was not to the Society of Jesus.[4]

Having spent nine months at Maredsous, in February 1913, Chapman was made temporary superior of the Caldey island community (now based at Prinknash Abbey), when it was received into the Roman Catholic Church in 1913-14.[5]

On the outbreak of World War I (1914–1918), Chapman first became a Professor of Theology at Downside Abbey, joining the many monks who had fled Maredsous to England.[6] In early 1915, when these monks moved to Ireland, he became army chaplain to the British forces. After initial training, his brigade arrived in France in July 1915. He lived in the trenches in autumn 1915, until a persistent knee injury led to him being sent to hospital in November 1915. After leaving hospital, he first was stationed at Boyton Camp, Wiltshire, for several months, and then returned to France. At the end of 1917, he was transferred to Switzerland, where multilingual chaplains were need for the POW camps. He remained here until the Armistice.[7]

In 1919 Chapman transferred his monastic stability to Downside Abbey. He spent most of 1919 to 1922 in Rome, though, working on a commission on the revision of the Vulgate translation of the Bible.[8] He returned to Downside in 1922, where in 1929 the community elected him as abbot.[5]

As 4th Abbot of Downside, during his short term of four years, cut short by his death on 7 November 1933, he carried on the work of abbots Cuthbert Butler and Leander Ramsay. He completed the transformation of Downside into a modern abbey in the mainstream of the Benedictine tradition and in 1933 became the founder of Worth Priory (which became independent of Downside in 1957 and Worth Abbey in 1965) when he bought the property, then called "Paddockhurst", from Viscount Cowdray.

John Chapman was thought by competent critics to be the greatest patristics scholar of his time. Reputedly he had read all 378 volumes of Migne. He not only read both Greek and Latin with facility, but also read and wrote French, Italian and German with ease. Many of his contributions to biblical scholarship and patristics have proved of lasting value, especially his work on Cyprian, John the Presbyter, and on the priority of the Gospel according to Matthew that, so Chapman argued in support of the early Church tradition, was the first Gospel account to have been written (see also Synoptic Problem).

Among the novices that Chapman clothed in the monastic habit was in 1932 John Bernard Orchard, who soon felt drawn to follow his Abbot into researching the priority of the Gospel according to Matthew in the light of the patristic evidence, and eventually, after also constructing a synopsis of the four Gospel accounts in Greek and English for the easier study of the compositional sequence Matthew-Luke-Mark-John that is supported by certain early Christian writers, produced what by hindsight may be considered a synthesis of his and his mentor's insights.

In his day Chapman was a much sought-after spiritual director and authority on prayer, the spiritual life and mystical theology. His writings remain of perennial value, especially his Spiritual Letters. An oft quoted advice of his was: "Pray as you can, not as you cannot!".